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(-) Description

Title :  CRYSTAL STRUCTURE OF CLASS A BETA-LACTAMASE TOHO-1
 
Authors :  A. S. Ibuka, Y. Ishii, K. Yamaguchi, H. Matsuzawa, H. Sakai
Date :  06 Sep 02  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Two-Domain Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Ibuka, Y. Ishii, M. Galleni, M. Ishiguro, K. Yamaguchi, J. M. Frere, H. Matsuzawa, H. Sakai
Crystal Structure Of Extended-Spectrum Beta-Lactamase Toho-1: Insights Into The Molecular Mechanism For Catalytic Reaction And Substrate Specificity Expansion
Biochemistry V. 42 10634 2003
PubMed-ID: 12962487  |  Reference-DOI: 10.1021/BI0342822
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE TOHO-1
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-BLA
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , SER A:130 , LYS A:234 , THR A:235 , GLY A:236 , SER A:237 , HOH A:1054 , HOH A:1057 , HOH A:1082 , HOH A:1142BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARELYS A:197 , GLU A:273 , ARG A:274 , ARG A:276 , HOH A:1027 , HOH A:1066 , HOH A:1087 , HOH A:1123 , HOH A:1188BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWARELYS A:82 , ARG A:274 , ARG A:276 , ASP A:277 , HOH A:1027 , HOH A:1055 , HOH A:1064 , HOH A:1089 , HOH A:1122 , HOH A:1161BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREALA A:52 , ARG A:178 , HOH A:1050 , HOH A:1074 , HOH A:1252 , HOH A:1272BINDING SITE FOR RESIDUE SO4 A 1004
5AC5SOFTWARELYS A:197 , GLU A:269 , GLN A:270 , HOH A:1240 , HOH A:1269BINDING SITE FOR RESIDUE SO4 A 1005
6AC6SOFTWARETRP A:229 , PRO A:252 , GLU A:254 , ASN A:255 , HIS A:256 , PHE A:290 , HOH A:1276 , HOH A:1284BINDING SITE FOR RESIDUE SO4 A 1006
7AC7SOFTWARELYS A:88 , HIS A:89 , ASN A:92 , HOH A:1070 , HOH A:1216BINDING SITE FOR RESIDUE SO4 A 1007
8AC8SOFTWAREILE A:108 , LYS A:111 , HIS A:112 , HOH A:1088 , HOH A:1125BINDING SITE FOR RESIDUE SO4 A 1008

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IYS)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:166 -Pro A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IYS)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLT1_ECOLX69-84  1A:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 1IYS)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:261
 aligned with BLT1_ECOLX | Q47066 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:261
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
           BLT1_ECOLX    31 NSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAERRRDILAAAAKIVTHGF 291
               SCOP domains d1iysa_ A: beta-Lactamase, class A                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1iysA00 A:27-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh........eee.hhhhh.....hhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iys A  27 NSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAERRRDILAAAAKIVTHGF 290
                                    36        46        56||      67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237||     248   ||  259       269       279       289 
                                                         57|                                                                                                                                                                                238|         252|                                    
                                                          59                                                                                                                                                                                 240          254
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IYS)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BLT1_ECOLX | Q47066)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0030655    beta-lactam antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BLT1_ECOLX | Q47066: 1bza 1iyo 1iyp 1iyq 1we4 2wyx 2xqz 2xr0 2zq7 2zq8 2zq9 2zqa 2zqc 2zqd 4bd0 4bd1 4c3q 4x69 5kmw 5ksc

(-) Related Entries Specified in the PDB File

1bza 1BZA CONTAINS THE CRYSTAL STRUCTURE OF TOHO-1 E166A MUTANT.